This is the classic parser look-ahead problem that gave rise to the C ungetch() function.

In this case, you would be better of using perl's nouce to read your file in paragraph mode (see perlvar:$/). Basically, if you set $/='', perl will read a paragraph (defined as a number of lines terminated by \n\n). You can then pass the entire section in to the appropriate sub, have it split it into lines and do it thing from there. Eg.

#! perl -slw
use strict;

sub section1{
      # Split into lines
    my @lines = split'\n', $_[0]; 
    print 'Section 1 got:', $_ for @lines;
}
sub section2{ print 'Section2', @_; } # placeholder code.

sub getconf{
    local $/= ''; # Set paragraph mode on *locally*
    while( <DATA> ) {
        section1( $_ ), next if /^\[Section1]/;
        section2( $_ ), next if /^\[Section2]/;
    }
}

getconf();


__DATA__
[Section1]
var1=one
var2=two
var3=three

[Section2]
user1:pass1:50
user2:pass2:51
[download]

Output

Section 1 got:[Section1]
Section 1 got:var1=one
Section 1 got:var2=two
Section 1 got:var3=three
Section2[Section2]
user1:pass1:50
user2:pass2:51
[download]